Setting up research theses

I am thinking about the process to pick up a thesis for a bioinformatics like this

1. State what I want: I would like to do a research about protein folding
2. State what can be done with it: A lot, but I will concentrate on its structure and a specific disease related to human beings.
3. State how its folding issue leading to the disease: I will build a simulation program for this
4. Explain how can it be *fixed* virtually: I don't know at present. But of course I have to build another program to simulate how the input data correct the issue in question.

Is there anything wrong about my workflow to produce a thesis ("Visualization of disease XXX at the protein structure level") ? Thank you bears a lot.

The first step in designing a research project should be to review the scientific literature to see what has been done in the area you would like to study and what the most important unanswered questions are. In the specific area of computer simulations of protein folding, there is a great wealth of information already available. For example, here's a short review article by Ken Dill from last year: